Effect of Farming System on Grain Composition and Immunogenic Potential of Ancient and Modern Durum Wheat Varieties

Organic farming is increasingly promoted as a sustainable alternative to conventional wheat production; however, its effects on grain quality and immunogenic potential remain insufficiently understood. This study evaluated the influence of the farming system (organic vs. conventional) on grain composition, technological quality traits, immunochemical reactivity, and immunogenic peptide profiles in 13 durum wheat varieties, including traditional and modern Tunisian varieties. Protein fraction content, amino acid composition, gluten-quality parameters, starch content, and immunochemical reactivity against anti-gliadin antibodies were determined. In addition, in vitro digestion followed by LC–MS/MS peptidomic analysis and epitope mapping was performed on representative ancient and modern varieties to investigate the release of celiac-disease-related immunogenic peptides after simulated gastrointestinal digestion. Protein content and quality traits were mainly genotype-dependent, with no consistent effect from the farming system across all varieties. Organic farming was associated with reduced starch accumulation (3.2–39.9% reduction) and lower immunochemical reactivity. Peptidomic analysis further revealed a reduced number and relative abundance (20.8–43.6% lower abundance) of immunogenic peptides in organically cultivated wheat compared with conventionally grown counterparts. This study highlights the significant interaction between the genotype and farming system, and provides a novel demonstration that organic management can reduce the abundance of celiac-disease-related immunogenic peptides, particularly in ancient varieties.